Hi Christoph, Is this correction answer to my question number 2, "Does the FM technique aim to extract a table potential for CG system from the atomistic system with matching the forces? Can we use this extracted FM potential table for CG simulations --- not IBI, just normal CG MD simulation? If so would you please let me know how can I use this potential table to run CG simulations and what files are needed for that?":
gmx grompp -f grompp.mdp - p topol.top -c confout.gro gmx mdrun -table table_CG_CG.xvg where confout.gro is GC configuration file, and table_CG_CG.xvg is the potential table extracted from FM technique. Thanks, Mohsen On Wed, Jul 21, 2021 at 11:56 AM Mohsen Farshad <[email protected]> wrote: > Thanks for the explanation. I have still some difficulty understanding the > process, and I have the following questions: > > 1. Are C6 and C12 are literally summed up ("+") or they are just combined > during the FM process --- essentially they have not ever gotten separated? > > 2. Does the FM technique aim to extract a table potential for CG system > from the atomistic system with matching the forces? Can we use this > extracted FM potential table for CG simulations --- not IBI, just normal CG > MD simulation? If so would you please let me know how can I use this > potential table to run CG simulations and what files are needed for that? > > Thank you, > Mohsen > > On Tue, Jul 20, 2021 at 5:07 PM Christoph Junghans <[email protected]> > wrote: > >> On Tue, Jul 20, 2021 at 8:47 AM Mohsen Farshad <[email protected]> >> wrote: >> > >> > Thanks for the explanation. I am a bit confused. Is there any repulsion >> term in the Votca potential? Would you please explain what kind of >> potential is that? >> >> Gromacs just has the C6 and C12 tables columns, but in the case of >> VOTCA we just add the C6 and C12 parts together and you can make one >> of them zero. >> (see >> https://manual.gromacs.org/documentation/2019.5/reference-manual/special/tabulated-interaction-functions.html#user-specified-potential-functions >> ) >> Basically because it is not easy to separate the C6 from the C12 part >> and also because you can do some funky things by using the C6 part for >> something else. >> >> > >> > Also in SPCE tutorial, to run CG simulation, it is suggested to use the >> files for ibi example. I have a few questions in regards to this part of >> the tutorial: >> > >> > 1. What command should I use to run coarse grain: >> > >> > "gmx grompp" and then "gmx mdrun -v" >> This runs a MD simulation directly only use that after coarse-graining >> or for atomistic simulation. >> >> > >> > or "csg_inverse --options settings.xml" >> This is the right command to do IBI >> >> > >> > 1. Would you explicitly explain how should I adjust the settings.xml to >> make it compatible with the potential table that comes from FM. The current >> IBI setting.xml uses IBI interactive algorithm. Is that needed to run CG >> simulation using FM potential? --- if setting.xml is not needed please >> ignore this question. >> >> FM is a different CG method than IBI. FM is one shot and done, while >> IBI is iterative. >> You could use the FM potential as a starting potential for IBI, but >> this is kind of pointless as FM matches the forces, while IBI matches >> the structure. >> >> > >> > 3. For CG simulation the CG configuration should be used or atomistic >> one? >> The CG one. >> >> Christoph >> >> > >> > Thank you, >> > Mohsen >> > >> > >> > On Mon, Jul 19, 2021 at 10:38 PM Christoph Junghans <[email protected]> >> wrote: >> >> >> >> On Mon, Jul 19, 2021 at 5:47 PM Mohsen Farshad < >> [email protected]> wrote: >> >> > >> >> > Here are the potential, force, and output potentials. Would you >> please let me know whether they are correct? >> >> The outcomes are actually correct. >> >> >> >> Your forces and the potential ends at 0.9nm and so is the xvg file. >> >> The values smaller than 0.9nm are not zero. >> >> We shift the potential in such a way that it is zero at the cutoff, >> >> hence all values for r> 0.9nm are zero. >> >> We put the values in the C12 column of the gromacs xvg table, hence >> >> columns 2-5 are empty and only columns 6+7 have numbers. >> >> >> >> Christoph >> >> > >> >> > Thank you, >> >> > Mohsen >> >> > >> >> > On Mon, Jul 19, 2021 at 6:34 PM Christoph Junghans < >> [email protected]> wrote: >> >> >> >> >> >> On Mon, Jul 19, 2021 at 3:04 PM Mohsen Farshad < >> [email protected]> wrote: >> >> >> > >> >> >> > Hi Christoph, >> >> >> > >> >> >> > I was able to install the Votca using Spack. However, going >> through the tutorial I confronted an error after executing the following >> command: >> >> >> > >> >> >> > csg_call table integrate CG-CG.force CG-CG.pot >> >> >> > >> >> >> > The last lines of the error is as follows: >> >> >> > >> >> >> > #000: >> /tmp/tuo98996/spack-stage/spack-stage-hdf5-1.10.7-3mcrng3jtezm72xs2i2fbwpwzogxsupf/spack-src/src/H5T.c >> line 1708 in H5Tcopy(): not a datatype or dataset >> >> >> > >> >> >> > major: Invalid arguments to routine >> >> >> > >> >> >> > minor: Inappropriate type >> >> >> > >> >> >> > Running subscript 'table_integrate.pl CG-CG.force CG-CG.pot' >> (from tags table integrate) dir >> /home/tuo98996/spack/opt/spack/linux-centos7-broadwell/gcc-9.3.0/votca-csg-stable-7slgbunnjcw6657pwdjeshozxpfzi3d5/share/votca/scripts/invers >> >> >> > >> >> >> > >> >> >> > The resulting CG table potential is zero for all the distances. >> >> >> The integrate script will only act on the first valid point, usually >> >> >> marked with "i" in the last column of the force table. >> >> >> So that might be the problem. Otherwise send us the force table and >> we >> >> >> can have a look as well. >> >> >> >> >> >> Christoph >> >> >> >> >> >> > >> >> >> > >> >> >> > Looking forward to your feedback, >> >> >> > >> >> >> > >> >> >> > Thanks, >> >> >> > >> >> >> > Mohsen >> >> >> > >> >> >> > >> >> >> > >> >> >> > >> >> >> > On Thu, Jul 15, 2021 at 7:02 PM Christoph Junghans < >> [email protected]> wrote: >> >> >> >> >> >> >> >> Can you run "spack cd -b votca-csg@stable" and look for a .log >> file in there? >> >> >> >> >> >> >> >> Christoph >> >> >> >> >> >> >> >> On Thu, Jul 15, 2021 at 2:42 PM Mohsen Farshad < >> [email protected]> wrote: >> >> >> >> > >> >> >> >> > On the cluster, the run is not ending now. In my own machine, >> it says: >> >> >> >> > >> >> >> >> > ==> Error: votca-csg-stable-t3g3evics7o4vvqtxxunsnx2p67u56bg: >> Package was not installed >> >> >> >> > >> >> >> >> > ==> Error: Installation request failed. Refer to reported >> errors for failing package(s). >> >> >> >> > >> >> >> >> > >> >> >> >> > The last comment on the cluster is following: >> >> >> >> > >> >> >> >> > [+] >> /home/tuo98996/spack/opt/spack/linux-centos7-haswell/gcc-4.8.5/gromacs-2019.6-xtfitykzurvzarvflpj2v6cu3wywr5fc >> >> >> >> > >> >> >> >> > >> >> >> >> > >> >> >> >> > On Thu, Jul 15, 2021 at 4:38 PM Christoph Junghans < >> [email protected]> wrote: >> >> >> >> >> >> >> >> >> >> On Thu, Jul 15, 2021 at 2:34 PM Mohsen Farshad < >> [email protected]> wrote: >> >> >> >> >> > >> >> >> >> >> > Hi Christoph, >> >> >> >> >> > >> >> >> >> >> > After cloning Spack I inserted the following commands on my >> own machine and the cluster, but neither machines were able to successfully >> complete the installation after a relatively long time. >> >> >> >> >> > >> >> >> >> >> > git clone https://github.com/spack/spack.git spack >> >> >> >> >> > source spack/share/spack/setup-env.sh >> >> >> >> >> > spack install votca-csg@stable >> >> >> >> >> > >> >> >> >> >> > Do you think there is something wrong with the compiler or >> I am missing some commands and installation is more complicated than I am >> thinking of? >> >> >> >> >> >> >> >> >> >> Can you post the error message? >> >> >> >> >> >> >> >> >> >> Christoph >> >> >> >> >> > >> >> >> >> >> > I have made sure the Spack is updated. >> >> >> >> >> > >> >> >> >> >> > Looking forward to hearing from you, >> >> >> >> >> > >> >> >> >> >> > Thanks, >> >> >> >> >> > Mohsen >> >> >> >> >> > >> >> >> >> >> > On Sat, Jul 10, 2021 at 10:01 AM Christoph Junghans < >> [email protected]> wrote: >> >> >> >> >> >> >> >> >> >> >> >> On Fri, Jul 9, 2021 at 3:52 PM Christoph Junghans < >> [email protected]> wrote: >> >> >> >> >> >> > >> >> >> >> >> >> > On Fri, Jul 9, 2021 at 3:42 PM Mohsen Farshad < >> [email protected]> wrote: >> >> >> >> >> >> > > >> >> >> >> >> >> > > Hi Votca developers, >> >> >> >> >> >> > > >> >> >> >> >> >> > > Is there a way to solve this issue without the need >> for installation of "votca@stable" using spack? >> >> >> >> >> >> > Not really, we really have to make a 2021.1 release and >> bump the spackage. >> >> >> >> >> >> > Alternatively, you could apply the code change of the >> patch >> >> >> >> >> >> > ( >> https://github.com/votca/tools/commit/6bb7e35ba7d1a31247eafb323be2777ec0439cfe >> ) >> >> >> >> >> >> > manually. >> >> >> >> >> >> > I also made a quick fix in spack: >> https://github.com/spack/spack/pull/24815 >> >> >> >> >> >> > Once that is merged, you should be good to go. >> >> >> >> >> >> The fix is part of spack now, just pull the latest version >> of spack >> >> >> >> >> >> and everything should be fine. >> >> >> >> >> >> >> >> >> >> >> >> > >> >> >> >> >> >> > Christoph >> >> >> >> >> >> > >> >> >> >> >> >> > > >> >> >> >> >> >> > > Thanks, >> >> >> >> >> >> > > Mohsen >> >> >> >> >> >> > > ---------- Forwarded message --------- >> >> >> >> >> >> > > From: [email protected] <Unknown> >> >> >> >> >> >> > > Date: Thursday, July 8, 2021 at 6:09:31 PM UTC-4 >> >> >> >> >> >> > > Subject: C++ Compiler issue >> >> >> >> >> >> > > To: [email protected] <Unknown> >> >> >> >> >> >> > > >> >> >> >> >> >> > > >> >> >> >> >> >> > > Hi Votca developers, >> >> >> >> >> >> > > >> >> >> >> >> >> > > My question: C++ Compiler issue: I am trying to >> install VOTCA on a supercomputer using spack. I am getting a C++ error. >> Could you please have a look at the attached log file? I am trying to >> figure out what my next steps are. >> >> >> >> >> >> > > >> >> >> >> >> >> > > Response from Christoph: The issue you found is >> already fixed (see >> >> >> >> >> >> > > https://github.com/votca/tools/pull/361), but not >> part of a release >> >> >> >> >> >> > > yet. >> >> >> >> >> >> > > You can install "votca@stable" using spack to get the >> fix. >> >> >> >> >> >> > > >> >> >> >> >> >> > > Apologies for the test email. >> >> >> >> >> >> > > >> >> >> >> >> >> > > Thank you >> >> >> >> >> >> > > Akash >> >> >> >> >> >> > > >> >> >> >> >> >> > > -- >> >> >> >> >> >> > > Join us on Slack: >> https://join.slack.com/t/votca/signup >> >> >> >> >> >> > > --- >> >> >> >> >> >> > > You received this message because you are subscribed >> to the Google Groups "votca" group. >> >> >> >> >> >> > > To unsubscribe from this group and stop receiving >> emails from it, send an email to [email protected]. >> >> >> >> >> >> > > To view this discussion on the web visit >> https://groups.google.com/d/msgid/votca/4ee1f111-852d-4526-9920-55cfe9b110e9n%40googlegroups.com >> . >> >> >> >> >> >> > >> >> >> >> >> >> > >> >> >> >> >> >> > >> >> >> >> >> >> > -- >> >> >> >> >> >> > Christoph Junghans >> >> >> >> >> >> > Web: http://www.compphys.de >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> -- >> >> >> >> >> >> Christoph Junghans >> >> >> >> >> >> Web: http://www.compphys.de >> >> >> >> >> >> >> >> >> >> >> >> -- >> >> >> >> >> >> Join us on Slack: https://join.slack.com/t/votca/signup >> >> >> >> >> >> --- >> >> >> >> >> >> You received this message because you are subscribed to >> the Google Groups "votca" group. >> >> >> >> >> >> To unsubscribe from this group and stop receiving emails >> from it, send an email to [email protected]. >> >> >> >> >> >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/votca/CAHG27e42Gj-VuA2sudLLec34W8J5RNuu0ocod9C8aee7jwoMEg%40mail.gmail.com >> . >> >> >> >> >> > >> >> >> >> >> > -- >> >> >> >> >> > Join us on Slack: https://join.slack.com/t/votca/signup >> >> >> >> >> > --- >> >> >> >> >> > You received this message because you are subscribed to the >> Google Groups "votca" group. >> >> >> >> >> > To unsubscribe from this group and stop receiving emails >> from it, send an email to [email protected]. >> >> >> >> >> > To view this discussion on the web visit >> https://groups.google.com/d/msgid/votca/CAAbE4DpAJGCt-_E9RLcOQOA8QQ0jDcsm4AyHtHVfGN4JMZiqdA%40mail.gmail.com >> . >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> -- >> >> >> >> >> Christoph Junghans >> >> >> >> >> Web: http://www.compphys.de >> >> >> >> >> >> >> >> >> >> -- >> >> >> >> >> Join us on Slack: https://join.slack.com/t/votca/signup >> >> >> >> >> --- >> >> >> >> >> You received this message because you are subscribed to the >> Google Groups "votca" group. >> >> >> >> >> To unsubscribe from this group and stop receiving emails from >> it, send an email to [email protected]. >> >> >> >> >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/votca/CAHG27e4cEtmjOuKO3QEMgoHsZSyAJ%3Dp5%2BPS2bihs25p6S%3DkZSA%40mail.gmail.com >> . >> >> >> >> > >> >> >> >> > -- >> >> >> >> > Join us on Slack: https://join.slack.com/t/votca/signup >> >> >> >> > --- >> >> >> >> > You received this message because you are subscribed to the >> Google Groups "votca" group. >> >> >> >> > To unsubscribe from this group and stop receiving emails from >> it, send an email to [email protected]. >> >> >> >> > To view this discussion on the web visit >> https://groups.google.com/d/msgid/votca/CAAbE4Dq6vsiEjqxsJGoVLawnA4VwPzLaCbO7zn3Avn2xJoa5rg%40mail.gmail.com >> . >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> -- >> >> >> >> Christoph Junghans >> >> >> >> Web: http://www.compphys.de >> >> >> >> >> >> >> >> -- >> >> >> >> Join us on Slack: https://join.slack.com/t/votca/signup >> >> >> >> --- >> >> >> >> You received this message because you are subscribed to the >> Google Groups "votca" group. >> >> >> >> To unsubscribe from this group and stop receiving emails from >> it, send an email to [email protected]. >> >> >> >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/votca/CAHG27e6UhCYcqbPEb5tNk7E4dS6-4OZGzmtA9tjc7zUNsAcg2A%40mail.gmail.com >> . >> >> >> > >> >> >> > -- >> >> >> > Join us on Slack: https://join.slack.com/t/votca/signup >> >> >> > --- >> >> >> > You received this message because you are subscribed to the >> Google Groups "votca" group. >> >> >> > To unsubscribe from this group and stop receiving emails from it, >> send an email to [email protected]. >> >> >> > To view this discussion on the web visit >> https://groups.google.com/d/msgid/votca/CAAbE4DqTUn3QnuN1QFwb6UBnouvgbFzAJWfb9YeuL8sPNc7LvQ%40mail.gmail.com >> . >> >> >> >> >> >> >> >> >> >> >> >> -- >> >> >> Christoph Junghans >> >> >> Web: http://www.compphys.de >> >> >> >> >> >> -- >> >> >> Join us on Slack: https://join.slack.com/t/votca/signup >> >> >> --- >> >> >> You received this message because you are subscribed to the Google >> Groups "votca" group. >> >> >> To unsubscribe from this group and stop receiving emails from it, >> send an email to [email protected]. >> >> >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/votca/CAHG27e67gFfpCoCrSE3LqRUd_JJkxhzrX%2BiZjaXqWPZL6KSTXQ%40mail.gmail.com >> . >> >> > >> >> > >> >> > >> >> > -- >> >> > Mohsen Farshad >> >> > Ph.D. Chemistry >> >> > University of Maine >> >> > >> >> > -- >> >> > Join us on Slack: https://join.slack.com/t/votca/signup >> >> > --- >> >> > You received this message because you are subscribed to the Google >> Groups "votca" group. >> >> > To unsubscribe from this group and stop receiving emails from it, >> send an email to [email protected]. >> >> > To view this discussion on the web visit >> https://groups.google.com/d/msgid/votca/CAAbE4Dr9PXU%3D7j4%3D0TP-azBAHucna2WoWpZxz%3DCGqReCrGnaFA%40mail.gmail.com >> . >> >> >> >> >> >> >> >> -- >> >> Christoph Junghans >> >> Web: http://www.compphys.de >> >> >> >> -- >> >> Join us on Slack: https://join.slack.com/t/votca/signup >> >> --- >> >> You received this message because you are subscribed to the Google >> Groups "votca" group. >> >> To unsubscribe from this group and stop receiving emails from it, send >> an email to [email protected]. >> >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/votca/CAHG27e43wNAE%2BD_a4NhA9sCmJT8O8rMd4JpTW-fHrHBU0oOLAg%40mail.gmail.com >> . >> > >> > -- >> > Join us on Slack: https://join.slack.com/t/votca/signup >> > --- >> > You received this message because you are subscribed to the Google >> Groups "votca" group. >> > To unsubscribe from this group and stop receiving emails from it, send >> an email to [email protected]. >> > To view this discussion on the web visit >> https://groups.google.com/d/msgid/votca/CAAbE4Doyh8wWXaPFoYxHtMPdnrMDA%2BjtBhnPmY3nE9X60asS2g%40mail.gmail.com >> . >> >> >> >> -- >> Christoph Junghans >> Web: http://www.compphys.de >> >> -- >> Join us on Slack: https://join.slack.com/t/votca/signup >> --- >> You received this message because you are subscribed to the Google Groups >> "votca" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected]. >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/votca/CAHG27e5X1WAuY55LbM3_o5JP2ubHRgJexuHoO0_89bn2YcXvzw%40mail.gmail.com >> . >> > > > -- > Mohsen Farshad > Ph.D. Chemistry > University of Maine > -- Mohsen Farshad Ph.D. Chemistry University of Maine -- Join us on Slack: https://join.slack.com/t/votca/signup --- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/votca/CAAbE4DpT89%2BR7m3%3DoFnT_JiEtV6Kx%3DuNSqohEZ5AW8bEBiFygg%40mail.gmail.com.
